Freesurfer

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30070 discussions

-autorecon2-wm: Inconsistency between recon-all code and documentation
by Antonin Skoch 10 Apr '17

10 Apr '17

Dear experts, I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh make white surfaces). But, in the code both -autorecon2-wm and -autorecon2-cp are equivalently processing stages 12-23. It seems to me that the stages 12-14 are not needed to process again in -autorecon2-wm (which is used for re-processing after editing wm.mgz). Could you please comment on? Regards, Antonin Skoch

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create mask from cluster number?
by lindsay hanford 10 Apr '17

10 Apr '17

Hello Freesurfer Developers, The main point of my post is to determine whether its possible to create a mask from a cluster ID run using a subset of the sample, and then use that mask to extract cortical thickness values from a model run with the full sample. I am running a pretty basic cortical thickness- behavioural correlation analysis with two groups using fsgd. Because I have a relatively small sample size (just over 40 participants in each group) I wanted to restrict my analysis to only regions that showed a relationship within the HC group. I ran the model using mri_glmfit: mri_glmfit --y HC.43.rh.10.mgh --fsgd Behav.fsgd --C v1.slope.mtx --surf fsaverage rh --cortex --glmdir MCCB.HC.43.rh Behav.fsgd setup: GroupDescriptorFile 1 Title MaineffectofGroup Class HC Variables BehavMC Input 128 HC -5 Input 132 HC 8 Input 192 HC -10 Input 193 HC -6 ... v1.slope.mtx: 0 1 *quick side question - in the past I was curious to see if this could test positive and negative relationships. I tried two different contrasts: 0 1 and 0 -1 to test the positive and negative relationships, respectively, however the results were the direct inverse of each other... it didn't show negative slope relationships. I am curious if its possible to test for negative relationships in freesurfer? How would you set up that contrast? next, I used mri_surfcluster to generate image and table files: mri_surfcluster --in HC.43.rh/v1.slope/sig.mgh --subject fsaverage --hemi rh --surf pial --annot aparc --thmin 2 --ocn HC.43.rh/v1.slope/results.ocn.mgh --sum HC.43.rh/v1.slope/results.sum.txt my results.sum.txt file shows a number of clusters ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 3.719 163035 270.33 57.7 -34.6 -21.5 234 inferiortemporal 2 3.499 22608 217.35 33.2 -48.2 -15.1 230 fusiform 3 3.170 2804 93.01 42.1 22.1 23.9 132 rostralmiddlefrontal Would it be possible to create a mask defined by say "ClusterNo 1"? Once the mask is created, I want to use it to extract the cortical thickness values for all participants (including those that weren't used to create the mask).. Is this possible? Can that be done using mri_segstats? Let me know if you require any other details. Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Thank you in advance, Lindsay

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dimension mismatch between source and mask
by Maria Hakonen 10 Apr '17

10 Apr '17

Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz However, I am getting an error " dimension mismatch between source and mask". Could someone please let me know how to solve this problem? Best, Maria

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Ventricle-to-Brain Ratio
by Gullickson, James 10 Apr '17

10 Apr '17

Hello all, I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go about this using the aseg.stats output (using asegstats2table), but am running into inconsistencies. The basic calculation for VBR is: (Total Ventricular Volume/Total Brain Volume) * 100 i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and neurodegeneration. *Frontiers in human neuroscience*, *7*, 395. What is the best way to get Total Ventricular Volume (TVV) and Total Brain Volume (TBV) for this calculation? I have tried several ways, which lead to different values: TVV = left lateral ventricle + left inf lateral ventricle + right lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th ventricle + 5th ventricle + choroid plexus which gives me a different result than TVV = BrainSegVol - BrainSegVolNotVent and for TBV TBV = TotalGrayVol + CorticalWhiteMatterVol which differs from TBV = BrainSegVolNotVent Thank you for your help, James Gullickson

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Re: [Freesurfer] white matter edits not incorporated.
by Octavian Lie 10 Apr '17

10 Apr '17

Dear All, I wanted to know if there is any take on the issue of white matter edits (specifically deleting unwanted voxels from wm.mgz). I sent a subject a week ago for your review. It seems this is a problem that I had with several scans, and by the message list, I am not the only one. Recent users having the same issues have raised the possibility of editing orig.mgz by replacing wm intensity with gm intensity in the troubled areas as workaround to the wm.mgz issue. Please let me know, Thank you, octavian Dear Bruce, I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on reruns using any of the recon-all -autorecon-wm -aitorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all FOr example, the complete command line for a rerun is recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 -parallel > output.txt & Here are some of the edited voxels which are not excluded from the wm on rerun: -40.14, -2.67, 116.29 coronal slice 132 12.73, -23.67, 126.16 coronal slice 171 14.05, 12.33, 11.61 coronal slice 147 I mention this is not the only subject where I have this problem. Thank you for your help.

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Re: [Freesurfer] A question regarding LUT/Freeview
by amir hosein 09 Apr '17

09 Apr '17

Dear Ruopeng, Thanks a lot for your reply. I am sorry, but I still could not fix this. Do you mean a command like this: freeview –v aparc+aseg.mgz:colormap=lut:isosurface=2032,2035 I could not perform what I have in mind using this command. I want to simultaneously show several different brain areas on a T1 image. The labels are so different; as examples, one is 14, one is 100, and one is 1250. Currently I am extracting labels, and using MATLAB I overlay them on a T1 image. I am sure Freesurfer should be able to nicely perform this, but this is not resolved for me yet :) Many thanks again, Amir

2 1

-hemi flag
by Nillo, Ryan Michael R 09 Apr '17

09 Apr '17

Hi FreeSurfer users, I am using FreeSurfer v5.3 and have noticed that when -hemi is used as a flag in recon-all, the half I did not specify is not present in wm.mgz. The full command is recon-all -autorecon2 -autorecon3 -hemi (l or r)h -subjid subject_name -sd SUBJECTS_DIR. After running, white matter is missing in the half of wm.mgz not specified under the -hemi flag, but the surfaces and segmentation in aparc+aseg are unaffected. Is this a bug? Ryan Michael Nillo UCSF Center for Radiology and Biomedical Imaging Staff Research Associate

1 0

QA Tool error when identifying aseg outliers
by Ladan Shahshahani 09 Apr '17

09 Apr '17

Dear all, I'm using QA_tools v1.2 to check the recon-all processes for my subjects. I'm getting the following lines in my terminal window while performing QA on some subjects: Processing each subcortical label ... (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error summary log says that there are 0 outliers for this subject. Is this because of the syntax error I get that no outliers are identified or there are really no outliers in my data? In the [Subject id]/scripts/recon_checker.log I see lines like the following: checking subcortical label: Epidermis, 0 +/- 0 checking subcortical label: Conn-Tissue, 0 +/- 0 checking subcortical label: SC-Fat/Muscle, 0 +/- 0 checking subcortical label: CSF-SA, 0 +/- 0 My question is what is "0 +/-0" telling me? What does it represent? Thanks in advance. Bests, Ladan

1 0

Freeview
by N Saf 08 Apr '17

08 Apr '17

Dear FreeSurfer experts, I have two questions please. 1- I cannot understand the concept of "existing labels". Why few labels (such as #19) do exist in the LUT, but they cannot be overlaid on the brain? What should I do if I need to map one of those labels on the brain that disappear when I press the button of "existing labels"? 2- I can see that the 11115 label is named as ctx-lh-G-front-middle, and the 1109 label is named as ctx-lh-G-frontal-middle. Is there any difference between these two? If yes, what is the difference? If no, why their name is different? (The 1109 label disappears when pressing the existing labels button) Sincerely yours, Nazanin

2 1

withdrawing from the mailing list.
by kjunji＠med.kanazawa-u.ac.jp 08 Apr '17

08 Apr '17

Dear Secretariat of Freesurfer mailing list I want to stop receiving emails from the Freesurfer mailing list. Please teach me to withdraw from the mailing list. Sincerely yours. Junji Komatsu in Kanazawa university hospital.

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